I know this is going to sound flippant, but look around for it. The CK probably placed it somewhere odd, like under the floor or in the wall behind you. I have had that happpen before. It happens quite a lot actually. If you double click on the item in the cell window, it will take you to it, but it might be behind something.
Sorry, that was slightly misleading >.<
The invisible item in question is a PlayerBookShelfTrigger, needed for all bookshelves, its the one that you have to cover the books with i believe. I've looked on the items list and it is there, and i've double clicked on it, hit 'T' etc but it just wont show. This is becoming an increasing problem for me since alot of things arn't loading in the Kit, including huge bits of mountain outside. It's really hindering the progress of my house. Personally i hate bookshelves i think they're a waste of resources and space, i prefer just to store books in a container in a house. However i do plan to upload this house to the Steam workshop and i know for a fact one of the first complaints from people who download it will be 'Why are there no bookshelves?
Though i just had a brain wave, wouldn't it work if i simply copied an entire bookshelf from the Breezehome Cell? Of course i may need to edit it a little bit.
EDIT: The above worked, it appeared when i copied it over, and the bookshelf is working now. However that problem is still there with the renfering unless i'm within 4 or 5 meters of it.